Google Season of Docs 2024 Proposal

[sneha9231]

PROPOSAL TITLE - Unifying the JuliaHeath Organization Documentation Landscape

About your organization

Note

In this section, tell us about your organization or project in a few short paragraphs. What problem does your project solve? Who are your users and contributors? How long has your organization or project been in existence? Give some context to help us understand why funding your proposal would create a positive impact in open source and the world.

The Julia Programming Language is an MIT-licensed high-performance programming language designed for speed, usability, and reproducibility within both scientific and general purpose computing.
Currently the Julia community has over 7,000 registered Julia packages, 35 million+ downloads of Julia, and thousands of contributors worldwide.
Julia's popularity continues to grow thanks to the dedicated community of users and developers who have helped develop several smaller specialty ecosystems within Julia.

In particular, the JuliaHealth Organization is one such ecosystem that was originally organized and founded 2020.
It is an organization dedicated to improving healthcare by developing open-source tools to work with a variety of health data and promotes interoperable data standards within the broader health research community.
The community is made up of health researchers, data scientists, software developers, and healthcare professionals who are passionate about using Julia to investigate and improve patient outcomes and promote data-driven decision-making.

Over the past four years, our organization membership has grown to more than 60 members actively working on the dozens of JuliaHealth packages we house.
As the entire JuliaHealth user community comprises more than 250 registered users across the Julia Slack and Julia Zulip instances, niche subecosystems have organically arisen under the JuliaHealth umbrella.
Currently, there are various subecosystems such as the Medical Imaging and the Observational Health subecosystem with more subecosystems beginning to emerge.

Your project’s problem

Note

Tell us about the problem your project will help solve. Why is it important to your organization or project to solve this problem?

With JuliaHealth's terrific growth over the years -- both in terms of growth in users, members, and actively maintained packages -- we are beginning to see the need for more unified documentation.
Without this unified documentation, we are seeing:

• User confusion due to the lack of documentation around subecosystems (including both emerging and established subecosystems)

• Developing fragmentation of documentation across packages

• Lack of clarity in how users and developers can compose packages together across JuliaHealth and the broader Julia ecosystem to accomplish research tasks

In some ways, this is a very good place to be in in that we have grown to the point of having these issues.
Users and developers want to engage with the JuliaHealth community, but if we do not provide a more unified documentation approach, we could potentially lose members or new contributors and stagnate our growth.

Project Impact

• By providing clearer guidance and improving accessibility, we seek to make navigating the different aspects of the JuliaHealth organization seamless and intuitive.
• We envision through participation in GSoD that by developing enhanced and unified documentation, we can assist all community levels within the JuliaHealth ecosystem.
• Additionally, as we construct solutions within JuliaHealth to address the needs we have encountered as a growing organization, we will share our insights to the broader Julia community to illustrate various methods other ecosystems within Julia can adapt to meet growing demand.

Your project’s scope

Note

Tell us about what documentation your organization will create, update, or improve. If some work is deliberately not being done, include that information as well. Include a time estimate, and whether you have already identified organization volunteers and a technical writer to work with your project.

Although there are many subecosystems within JuliaHealth, our project will be scoped to specifically the Medical Imaging subecosystem as it has grown mature enough to encounter many of these problems already.
Working on documentation around the Medical Imagining subecosystem will benefit the rest of the JuliaHealth ecosystem as it will provide a roadmap for how other subecosystems can best document themselves and support their users.

To better position the Medical Imaging subecosystem within the JuliaHealth organization, we will first have to do some general documentation improvements to the main JuliaHealth website.
This includes:

• Upgrade website to latest Julia documentation deployment tool
  • DocumenterVitepress.jl may be one target
• Add additional organization details for JuliaHealth overall including:
  • A new landing page for the subecosystems
    • Medical Imaging
    • Observational Health
    • Standards and Interoperability
  • Package breakdown using our pre-existing package listing tool
• Add FAQ or support page
• Define and implement tracking metrics to monitor user engagement and interaction with the platform
  • Using an open source and GDPR compliant technology like GoatCounter

Once this initial groundwork is done, we will then address some of the specific core tooling within the Medical Imaging subecosystem.
Due to the modular nature of packages within this subecosystem, we will need to improve documentation across various packages to show what they should be used for, how they integrate with one another, and how to onboard as a potential new contributor:

• Documentation tasks for MedImage

  • Introduction to the theory of medical imaging formats and spatial metadata
  • Describe how to load and save image
  • Describe how apply basic transformation using MedImage

• Documentation tasks for MedEye3d

  • Write tutorial how to configure window size and amount of space allocated to text
  • Give detailed tutorial describing the possible configurations using TextureSpec objects
  • Add the section with all keyboard shortcuts and print screens showing their effects
  • Describe possible user interactions including:
    • Using tool with REPL for fast debugging, include how to modify and refresh image manually
    • Describe manual interaction of modifiable masks

• Documentation tasks for MedEval3D

  • Describe different metrics and what are their strength and weaknesses
  • Make a tutorial showing how to use each metric

• Documentation tasks for MedPipe3D

  • Describe how to use Medpipe functionalities in different use cases
  • Give introduction to the functionalities in development like augmentations, largest component analysis or hyperparameter tuning (without usage examples)

• Documentation tasks for KomaMRI:
  Where possible in the scope of these documentation tasks, we will link to or show how to integrate with other Julia packages within JuliaHealth or from the broader Julia community such as JuliaImages or JuliaMRI.
  Related Issues to work on

Finally, if time permits, there will be some additional stretch goals that we would like to attempt accomplishing:

• Page for ongoing projects across JuliaHealth
• Page for research accomplishments within JuliaHealth
• Write a JuliaHealth blog entry on a Medeye topic to broaden project reach

Technical Writer

Name : Sneha Pandey
Description:
Sneha Pandey is a sophomore specializing in AI and ML and also serve as a Microsoft Learn Student Ambassador. Through this role, she had refined her ability to communicate complex concepts effectively to diverse audiences. Additionally, She had gained experience as a content writer, crafting content for my college. She has hands-on experience in developing various mini projects, such as a WhatsApp bot and ML captioning models using Streamlit and Python. Her familiarity with Julia stems from previous engagements in medical imaging alongside MD PhD Msc Mitura. Moreover, She ensured comprehensive documentation of her personal projects using Documenter.jl. These experiences collectively equip her with the skills and proficiency required to excel as a technical writer.

Volunteer's Role

Volunteer 1: General JuliaHealth Organization Volunteer:
Name: Jacob S. Zelko
Duties:

1. Providing support for general JuliaHealth documentation tasks.
2. Assisting in reviewing documentation pull requests (PRs) periodically.
3. Deploying documentation within the Julia ecosystem as needed.
4. Handling miscellaneous tasks as they arise.
5. Serving as a general support role while integrating Technical Writer's work into the broader JuliaHealth ecosystem.

Volunteer 2: JuliaDocs and Documentation Deployment Volunteer:
Name: Anshul Singhvi
Duties:

1. Transition support the main JuliaHealth page to the designated technology platform.
2. Provide guidance on safely implementing tracking metrics to monitor user engagement and interaction with the platform.
3. Offer technical consultation and guidance as needed throughout the project duration.
4. Help fix issues or rememdy needs that may arise from using tools from within the JuliaDocs ecosystem

Volunteer 3: Medical Imaging Subecosystem Volunteer:
Name: Guillermo Sahonero Alvarez
Duties:

1. Provide guidance on medical imaging theory and spatial metadata
2. Support in connecting imaging discussions to other aspects of the Julia ecosystem (such as MLJ or JuliaImages)
3. Provide subject matter expertise on imaging standards
4. Assist in writing theorethical introductions

Volunteer 4: Task consultations on packages functionalities and function documentations
Duties :

1. Support for technical writer related to practical development issues of Julia programming languages
2. To help checking weather docstrings of functions are working correctly
3. Collaborate with KormaMRI to create specialized documentation sections based on their research paper, covering advanced topics or techniques relevant to medical imaging.

Work that is out of scope for this project:

To explicitly enumerate what work is out of scope for this project, we do not plan for work done in the following spaces:

• Developing thorough documentation for other subecosystems
• Any of the aforementioned medical imagining packages not related to documentation
  • Adding docstrings or crosslinks may fall in scope depending on the needs per task

Measuring your project’s success

Note

How will you know that your new documentation has helped solve your problem? What metrics will you use, and how will you track them?

Currently, the documentation we do have does not yet have support for documentation traffic analytics.
As of this moment, our best direct source for traffic metrics is to use JuliaHub to monitor package downloads and also to reference GitHub stars for a loose approximation of "discoverability".
Additionally, we take advantage of the The Julia Programming Language YouTube Channel that we use to monitor engagement with our recorded JuliaHealth Workgroup meetings.
In these situations, potential users or contributors would have to know where to look to find these resources or entry points to our supported packages and their respective subecosystems.

We would consider the project successful if :

For JuliaHealth, we would consider this project successful if:

• We can readily track documentation traffic across packages

  • Encompasses deploying a safe traffic detection tool
  • Seeing at least a 10 - 15% growth in traffic after the deployment of tracking

• An overall increase by 5 - 10% in traffic across all JuliaHealth platforms

  • Includes JuliaHub, YouTube, GitHub, and documentation statistics

• Most (if not all) enumerated documentation tasks are completed for the Medical Imaging subecosystem

  • Some Related Issue Links:
    Sub-Package Documentation 1
    Sub-Package Documentation 2
    Sub-Package Documentation 3
    Sub-Package Documentation 4

• At least 3 - 5 new active JuliaHealth contributors across the JuliaHealth ecosystem are onboarded

  • Tracked across GitHub contribution history

• A new blog post is published

Timeline

Note

How long do you estimate this work will take? Are you able to breakdown the tech writer tasks by month/week?

We assume the tech writer will put in part time hours (10-20 hours/week) during this time.

Monthly Plan

Dates	Action items
May	Technical writer and volunteers are hired, onboarding
June-July	Research into Julia community, Audit existing documentation
August-September	Create Standard Package Documentations, Medical imaging subecosystem documentation
October	Improvements to the main page of JuliaHealth
November	Write a blog post, Any outstanding tasks or stretch goals

Weekly Plan

Week (1-2) - Reading and Familiarization
Week (3-4) - Documentation Traffic Tracker Setup
Week (5-7) - Setting up the environment and Updating Organization Details & Creating Subecosystem Sections
Week (8-10) - Linking Packages across subecosystems
Week (11- 16) - Medical Imaging Subecosystem Packages Documentation
Week (17- 20) - Review and Finalize Website Content also Feedback Incorporation
Week (20-24) - Wrap up / touch up of overall packages docs page alongside stretch goals

This timeline is largely accurate but we expect that different packages or tasks may be slightly more challenging than others.
The November time period gives us the opportunity to revisit any unfinished tasks and to potentially explore stretch goals if there were not many outstanding tasks left.

Communication Plan:

The primary communication channel we will use is Julia Slack and Dr. Jakub Mitura (MD, PhD) will be the individual responsible for all contact and mentoring throughout the project for regular updates and meetings.
Outside of Slack, email will be used to handle communications with GSoD organizers and administrators with Jakub Mitura's email being: jakub.mitura14@gmail.com.
Volunteers will also be available for communication on the Slack on an as-needed basis.
Additionally, project updates will be given through the Julia Health Slack Channel which is where the majority of JuliaHealth communication takes place between members, users, and the rest of the Julia community.

Project Budget

Note

You can include your budget in your proposal or as a separate link. If your budget is fewer than ten items, we recommend including it in your proposal.

Budget item	Amount	Running total
Technical writer	$4000	$4000
Volunteer (500x4)	$2000	$6000
Swags (3 shirts and 10 sticker packs)	$125	$6125
TOTAL		$6125

Additional justifications:

• Volunteers: Please see the above section on Project Scope for details about selected volunteers
• Swag: is to create a more welcoming environment for our writer and volunteers
  • Sticker packs will also be given to welcome new contributors

Additional information:

Note

Beyond the above proposal information, some additional notes about the composition of this project team:

Jacob Zelko was selected as a volunteer as he has a proven track record as a successful Google Summer of Code mentor for the past 3 years and is currently the Julia Organization's co-administrator for this years Google Summer of Code where he handles questions from both students and mentors.
Given his experience, Jacob will provide guidance to Jakub and Sneha as needed to make sure this project is well-aligned with general Google Open Source program goals.
Additionally, Jacob has a overseen many grants in the past through Google Summer of Code and former positions at Georgia Tech Research Institute and the Centers for Disease Control and will provide a valuable asset in answering any questions about the project scope.

Anshul Singhvi is a former Google Summer of Code student and has a vast swath of experience of working across the Julia ecosystem.
In particular, Anshul has membership with numerous Julia organizations and will be a crucial asset to not only what are best practices for documentation deployment but can also help with how to best unify JuliaHealth packages within JuliaHealth itself and potentially across the greater Julia landscape.
His insight will be crucial to mitigate any redundant work or answer oustanding questions to make sure this project is ran as effectively as possible.
Also, given Anshul's tremendous experience in delivering contract work, he will be key in making sure the metrics we investigate and report on for the case study in our final report will be done rigorously and to the best of the technical writer's ability given the data we have access to.

About Mentor
MD PhD Msc Jakub Mitura Researcher specialising in creating artificial intelligence models for medical imaging. Holds a doctorate in medical sciences with a thesis titled ‘The Role of Positron Emission Tomography Using Fluorodeoxyglucose in the Diagnosis of Vascular Prosthesis Infections.’ Additionally, holds a master’s degree in informatics with a specialisation in Big Data. Has authored scientific publications in the fields of medicine and artificial intelligence.

[TheCedarPrince]

Hi @sneha9231 and @jakubMitura14:

I did a more thorough review of the proposal so far and here are my thoughts. I grouped up thoughts by each heading you had originally:

About your organization

@sneha9231, you and I largely talked about this over Slack but the biggest point I was thinking about was emphasizing Julia programming language organization --> JuliaHealth --> Subecosystem and the history of JuliaHealth (a little bit).

Your Project's Problem

Inline with what I was mentioning in our group conversation yesterday, I would suggest reframing this to be slightly more broad. Here is how I would do it:

• Discuss how JuliaHealth is growing and needs more coordinated documentation (also maybe mention somehow that this is a great thing!)
• Mention that the emergence of subecosystems has both helped unify efforts but also could lead to fragmentation if no coordination happens
  • Mention that the medical imaging subecosystem is one leading
• This fragmentation could potentially lead to new Julians having to turn away from Julia entirely if we don't do something.

Project Impact

Here, you could then frame this section to say that by starting with general improvements to JuliaHealth, you could then use the medical imaging subecosystem to explore how to harmonize documentation across the rest of JuliaHealth (given your expertise with that subecosystem). As I mentioned over slack, to make this even more salient both to JuliaHealth and Julia overall is that as you test out novel approaches, you'll create new issues or can share suggestions for the rest of the Julia organization.

Project Scope

I see that there is quite a fair bit of project scope already so I will only make a few suggestions for the general JuliaHealth ecosystem (up to you @sneha9231 and @jakubMitura14 as to how you'd want to incorporate this):

1. JuliaHealth organization website

• Migrate website to DocumenterVitepress
• Add new organization details for JuliaHealth overall
• Create new sections for subecosystems
  • Medical Imaging
  • Observational Health
  • Standards and Interoperability
• Link to packages across JuliaHealth for proper subecosystem (maybe; may be out of scope)
• Page for research accomplishments within JuliaHealth (maybe; may be out of scope)
• Start FAQ page (maybe; may be out of scope)

2. Medical Imaging Subecosystem packages

• You'll probably need to add a task about using Documenter or DocumenterVitepress for this to stand up documentation

3. Set-up documentation traffic tracker (Goatcounter?)

• Also include privacy disclaimers where applicable

Also very important is who can volunteer to help with giving guidance. Here's who you could put down as volunteers right now:

• @TheCedarPrince: JuliaHealth Documentation volunteer
• Carlos's student: Medical imaging subecosystem documentation volunteer for KomaMRI and their techniques
• Anshul (Maybe): Julia Documentation Deployment volunteer

For Carlos's student, I would suggest reaching out to Carlos over Slack as well as Anshul to see if they would be interested/how to put them here. @jakubMitura14, you might want to be the one to reach out here. Also here, you might want to enumerate exactly how each volunteer will support the technical writer -- this will justify both their budget as well as clarify their responsibilities.

Measuring your project’s success

I think you should mention that some of the documentation does exist but we have not been able to readily run traffic analytics across the documentation alongside what you already wrote.

Also, keeping the case study you will eventually have to do in mind, please mention how you will track tasks being done, how they will be made public, and how you will use your experiences through keeping a form of project log to inform your case study.

We would consider the project successful if :

I think this is quite solid. Including things like the ability to track documentation traffic and user engagement with the blog would be great.

Timeline

That seems really great! I would actually suggest making the hours be more like 10 - 20hrs/week as this I have found is more realistic when working with part time students. Some weeks you'll have several hours worked over the time limit, others maybe less due to sickness, classes, etc. It generally balances out towards the end.

Monthly Plan

You'll probably need to revise this with my suggestions and our group discussion

Weekly Plan

REALLY GOOD! But like I was saying in the previous section, you'll probably need to revise this with my suggestions and our group discussion

Communication Plan:

Great!

Project Budget

Technical writer budget looks alright but I would suggest bumping this up to $4000 in line with my comment on timeline.

For volunteers, here is how I would break it down:

1. TheCedarPrince: $500
2. Carlos's student: $500
3. Anshul: $500

So you'd then have the total being: $5500 USD

Contact Information

Great! Maybe mention the health and medicine channel too

Final thoughts

Overall, this is really really great. I think it will take a fair amount of additional polishing but to me, I think it is doable. Ping me if you have any additional questions!

Also, I can help with a full in-depth proposal review again if you can get it to me by April 1st!

[cncastillo]

As I said during today's JuliaHealth meeting, I think it could be good to link the progress (measuring your project’s success) based on the completion of some issues (above 80%?). So some of the bullet points above can be transformed into issues.

Regarding potential volunteers, I have two candidates (@gsahonero and @depedraza). People here in Chile are very enthusiastic! 😄 Both are knowledgeable in medical imaging, focusing on MRI (they have used Julia and KomaMRI.jl), but they are happy to help with whatever is needed. My understanding is that @gsahonero is already in talks with @jakubMitura14, but @depedraza would also be interested in contributing if possible.

[gsahonero]

Hi! Yes, I'm interested and looking forward to collaborating with you!

[depedraza]

Hello there, yeah, just like as @gsahonero, I'd be thrilled to have the chance to collaborate with you guys! :)

[jakubMitura14]

Hello I am happy that there is so much enthusiasm @gsahonero @gsahonero I do not think I can add more volounteers (most budget must be allocated to main technical writer ). Hovewer if you would be still interested in collaboration I have multiple projects that require help, however I have no funding for them.
As to changing into the issues @cncastillo I will look into this; thanks!

[TheCedarPrince]

Feedback:

# PROPOSAL TITLE - Unifying the [JuliaHeath Organization](https://github.com/JuliaHealth) Documentation Landscape

[jakubMitura14]

good idea !

[TheCedarPrince]

Feedback:

About your organization

Note

In this section, tell us about your organization or project in a few short paragraphs. What problem does your project solve? Who are your users and contributors? How long has your organization or project been in existence? Give some context to help us understand why funding your proposal would create a positive impact in open source and the world.

The Julia Programming Language is an MIT-licensed high-performance programming language designed for speed, usability, and reproducibility within both scientific and general purpose computing.
Currently the Julia community has over 7,000 registered Julia packages, 35 million+ downloads of Julia, and thousands of contributors worldwide.
Julia's popularity continues to grow thanks to the dedicated community of users and developers who have helped develop several smaller specialty ecosystems within Julia.

In particular, the JuliaHealth Organization is one such ecosystem that was originally organized and founded 2020.
It is an organization dedicated to improving healthcare by developing open-source tools to work with a variety of health data and promotes interoperable data standards within the broader health research community.
The community is made up of health researchers, data scientists, software developers, and healthcare professionals who are passionate about using Julia to investigate and improve patient outcomes and promote data-driven decision-making.

Over the past four years, our organization membership has grown to more than 60 members actively working on the dozens of JuliaHealth packages we house.
As the entire JuliaHealth user community comprises more than 250 registered users across the Julia Slack and Julia Zulip instances, niche subecosystems have organically arisen under the JuliaHealth umbrella.
Currently, there are various subecosystems such as the Medical Imaging and the Observational Health subecosystem with more subecosystems beginning to emerge.

[jakubMitura14]

good!

[TheCedarPrince]

Feedback:

Your project’s problem

Note

Tell us about the problem your project will help solve. Why is it important to your organization or project to solve this problem?

With JuliaHealth's terrific growth over the years -- both in terms of growth in users, members, and actively maintained packages -- we are beginning to see the need for more unified documentation.
Without this unified documentation, we are seeing:

• User confusion due to the lack of documentation around subecosystems (including both emerging and established subecosystems)

• Developing fragmentation of documentation across packages

• Lack of clarity in how users and developers can compose packages together across JuliaHealth and the broader Julia ecosystem to accomplish research tasks

In some ways, this is a very good place to be in in that we have grown to the point of having these issues.
Users and developers want to engage with the JuliaHealth community, but if we do not provide a more unified documentation approach, we could potentially lose members or new contributors and stagnate our growth.

[jakubMitura14]

good!

[TheCedarPrince]

Feedback:

Project Impact

By providing clearer guidance and improving accessibility, we seek to make navigating the different aspects of the JuliaHealth organization seamless and intuitive.
We envision through participation in GSoD that by developing enhanced and unified documentation, we can assist all community levels within the JuliaHealth ecosystem.
Additionally, as we construct solutions within JuliaHealth to address the needs we have encountered as a growing organization, we will share our insights to the broader Julia community to illustrate various methods other ecosystems within Julia can adapt to meet growing demand.

I am not so sure if I like what I wrote -- did they want any more clarity beyond this?

[jakubMitura14]

I think it sounds good; like corporate language for google :D

[sneha9231]

so true, +1 @jakubMitura14 :)

[TheCedarPrince]

Feedback:

Your Project’s Scope

Note

Tell us about what documentation your organization will create, update, or improve. If some work is deliberately not being done, include that information as well. Include a time estimate, and whether you have already identified organization volunteers and a technical writer to work with your project.

Although there are many subecosystems within JuliaHealth, our project will be scoped to specifically the Medical Imaging subecosystem as it has grown mature enough to encounter many of these problems already.
Working on documentation around the Medical Imagining subecosystem will benefit the rest of the JuliaHealth ecosystem as it will provide a roadmap for how other subecosystems can best document themselves and support their users.

To better position the Medical Imaging subecosystem within the JuliaHealth organization, we will first have to do some general documentation improvements to the main JuliaHealth website.
This includes:

• Upgrade website to latest Julia documentation deployment tool
  • DocumenterVitepress.jl may be one target
• Add additional organization details for JuliaHealth overall including:
  • A new landing page for the subecosystems
    • Medical Imaging
    • Observational Health
    • Standards and Interoperability
  • Package breakdown using our pre-existing package listing tool
• Add an FAQ or support page
• Define and implement tracking metrics to monitor user engagement and interaction with the platform
  • Using an open source and GDPR compliant technology like GoatCounter

Once this initial groundwork is done, we will then address some of the specific core tooling within the Medical Imaging subecosystem.
Due to the modular nature of packages within this subecosystem, we will need to improve documentation across various packages to show what they should be used for, how they integrate with one another, and how to onboard as a potential new contributor:

• Documentation tasks for MedImage:

  • Introduction to the theory of medical imaging formats and spatial metadata
  • Describe how to load and save image
  • Describe how apply basic transformation using MedImage

• Documentation tasks for MedEye3d:

  • Write tutorial how to configure window size and amount of space allocated to text
  • Give detailed tutorial describing the possible configurations using TextureSpec objects
  • Add the section with all keyboard shortcuts and print screens showing their effects
  • Describe possible user interactions including:
    • Using tool with REPL for fast debugging, include how to modify and refresh image manually
    • Describe manual interaction of modifiable masks

• Documentation tasks for MedEval3D:

  • Describe different metrics and what are their strength and weaknesses
  • Make a tutorial showing how to use each metric

• Documentation tasks for MedPipe3D:

  • Describe how to use Medpipe functionalities in different use cases
  • Give introduction to transforms that are supported (or will be)
    • Include descriptions on various transforms that are supported
      * Brightness transform
      * Contrast augmentation transform
      * Gamma Transform
      * Gaussian noise transform
      * Rician noise transform
      * Mirror transform
      * Scale transform
      * Gaussian blur transform
      * Simulate low-resolution transform
      * Elastic deformation transform
    • Describe concept k fold cross validation and ensembling resulting models
    • Describe probabilistic oversampling for image segmentation
    • Describe why different images needs to be modified to have the same spacing origin and orientation
    • Describe what is the largest component analysis
    • Give short introduction to hyperparameter tuning and usage of Hyperopt package

• Documentation tasks for KomaMRI:

Where possible in the scope of these documentation tasks, we will link to or show how to integrate with other Julia packages within JuliaHealth or from the broader Julia community such as JuliaImages or JuliaMRI.

Finally, if time permits, there will be some additional stretch goals that we would like to attempt accomplishing:

• Page for ongoing projects across JuliaHealth
• Page for research accomplishments within JuliaHealth
• Write a JuliaHealth blog entry on a Medeye topic to broaden project reach

Technical Writer

TODO: You need to add a description about Sneha here
TODO: Review this section about filling in this section https://developers.google.com/season-of-docs/docs/tech-writer-selection#assess-tw
TODO: Review this section about https://developers.google.com/season-of-docs/docs/tech-writer-collaboration
TODO: Review this seciton as well: https://developers.google.com/season-of-docs/docs/tech-writer-collaboration

1. Familiarity with Documenter.jl and DocumenterVitepress
2. Basic knowledge of Medpipe3d packages

Volunteers and Roles

Volunteer 1: General JuliaHealth Organization Volunteer:

Name: Jacob S. Zelko
Duties:

1. Providing support for general JuliaHealth documentation tasks.
2. Assisting in reviewing documentation pull requests (PRs) periodically.
3. Deploying documentation within the Julia ecosystem as needed.
4. Handling miscellaneous support tasks as they arise.
5. Serving as a general support role while integrating Technical Writer's work into the broader JuliaHealth ecosystem.

Volunteer 2: JuliaDocs and Documentation Deployment Volunteer:

Name: Anshul Singhvi
Duties:

1. Transition support the main JuliaHealth page to the designated technology platform.
2. Provide guidance on safely implementing tracking metrics to monitor user engagement and interaction with the platform.
3. Offer technical consultation and guidance as needed throughout the project duration.
4. Help fix issues or rememdy needs that may arise from using tools from within the JuliaDocs ecosystem

Volunteer 3: Medical Imaging Subecosystem Volunteer:

Name:
Duties:

1. Provide guidance on medical imaging theory and spatial metadata
2. Support in connecting imaging discussions to other aspects of the Julia ecosystem (such as MLJ or JuliaImages)
3. Provide subject matter expertise on imaging standards

Out of Scope Work:

To explicitly enumerate what work is out of scope for this project, we do not plan for work done in the following spaces:

• Developing thorough documentation for other subecosystems
• Any of the aforementioned medical imagining packages not related to documentation
  • Adding docstrings or crosslinks may fall in scope depending on the needs per task

I have some major concerns for MedPipe3D. Why are these methods all enumerated? If you are not providing code examples, why do we need them? Why are you talking about probabilities and cross validation? Those tasks feel particularly out of scope and also duplicative. I think they would be very much strengthened by including code to show how these methods can be used. Did I misinterpret something here?

I do not know the name of volunteer 3 -- could you add it?

I removed the original volunteer 3 as that is not what the role of what a volunteer should be doing. They can certainly assist or provide support to a technical writer but with the amount of tasks that they were to assist with, it looks like they'd be more like a technical writer. Did you envision some thing else and this was just not included?

Finally, since @sneha9231 is our technical writer, there needs to be a section that more describes her background.

[TheCedarPrince]

Also, for stretch goals, could you add this line:

• Providing some initial guidance for how other subecosystems can unify their documentation

[jakubMitura14]

We will definitely add this stretch goal

As to volounteers let's divide it a bit
Let's add to volonteer 3 point

Collaborate with KormaMRI to create specialized documentation sections based on their research paper, covering advanced topics or techniques relevant to medical imaging.

I do not know any more details about it

Let's add to volounteer3

create specialized documentation sections based on KormaMRI research paper

Let's remove from volounteer 4 Korma and add

Support for technical writer related to practical development issues of Julia programming languages

Idea is volounteer 4 is for theory and 4 is programmer to help check docstrings

[TheCedarPrince]

Hm. This is much better but with the line:

Collaborate with KormaMRI to create specialized documentation sections based on their research paper, covering advanced topics or techniques relevant to medical imaging.

I don't like the word collaboration as it makes me think they'll be doing writing as opposed to advising our technical writer. I might suggest we loop in @cncastillo to this to help with delineating some specific tasks for KomaMRI since that is the only part left in this proposal that is very vague to me. How I see it is that our technical writer should be translating work from this paper into clearly defined sections for the documentation around KomaMRI. I just don't know what those sections are which is where the volunteers can assist.

---

Just to be clear when you say:

Support for technical writer related to practical development issues of Julia programming languages

So like helping provide code examples and that sort of thing? If so, that is a perfect angle -- I know you @jakubMitura14 will provide guidance for the 3D packages so having volunteers to do similar for Koma's suite of packages would be superb.

[jakubMitura14]

I do not think we would be able to wait for Komamri to wait

[jakubMitura14]

And yes we can add here about code examples; and I was thinking more about Div as fourth volounteer he already knows my packages and somewhat others

[TheCedarPrince]

Feedback:

Measuring your project’s success

Note

How will you know that your new documentation has helped solve your problem? What metrics will you use, and how will you track them?

Currently, the documentation we do have does not yet have support for documentation traffic analytics.
As of this moment, our best direct source for traffic metrics is to use JuliaHub to monitor package downloads and also to reference GitHub stars for a loose approximation of "discoverability".
Additionally, we take advantage of the The Julia Programming Language YouTube Channel that we use to monitor engagement with our recorded JuliaHealth Workgroup meetings.
In these situations, potential users or contributors would have to know where to look to find these resources or entry points to our supported packages and their respective subecosystems.

For JuliaHealth, we would consider this project successful if:

• We can readily track documentation traffic across packages
  • Encompasses deploying a safe traffic detection tool
  • Seeing at least a 10 - 15% growth in traffic after the deployment of tracking
• An overall increase by 5 - 10% in traffic across all JuliaHealth platforms
  • Includes JuliaHub, YouTube, GitHub, and documentation statistics
• Most (if not all) enumerated documentation tasks are completed for the Medical Imaging subecosystem
• At least 3 - 5 new active JuliaHealth contributors across the JuliaHealth ecosystem are onboarded
  • Tracked across GitHub contribution history

I rather updated the scope to be much more metrics focused. When the case study takes place, I will be available to assist in how to find these statistics. Let me know if this is too much or out of scope in your opinion Jakub and Sneha

[jakubMitura14]

Absolutely fantastic ideas !

[TheCedarPrince]

Feedback:

Timeline

Note

How long do you estimate this work will take? Are you able to breakdown the tech writer tasks by month/week?

We assume the tech writer will put in part time hours (10-20 hours/week) during this time.

Monthly Plan

Dates Action items
May Technical writer and volunteers are hired, onboarding
June-July Research into Julia community, Audit existing documentation
August-September Create Standard Package Documentations, Medical imaging subecosystem documentation
October Improvements to the main page of JuliaHealth
November Any outstanding tasks or stretch goals

Weekly Plan

Week (1-2) - Reading and Familiarization Week (3-4) - Documentation Traffic Tracker Setup Week (5-7) - Setting up the environment and Updating Organization Details & Creating Subecosystem Sections Week (8-10) - Linking Packages across subecosystems Week (11 - 16) - Medical Imaging Subecosystem Packages Documentation Week (17-20) - Review and Finalize Website Content also Feedback Incorporation Week (20-24) - Wrap up / touch up of overall packages docs page alongside stretch goals

This timeline is largely accurate but we expect that different packages or tasks may be slightly more challenging than others.
The November time period gives us the opportunity to revisit any unfinished tasks and to potentially explore stretch goals if there were not many outstanding tasks left.

i tweaked the weekly timeline a little bit in alignment with how we changed the scope earlier. Let me know what you think

[jakubMitura14]

Yes it is ok you did not added anything in time of Sneha exams :)

[TheCedarPrince]

Last bit of feedback:

Communication Plan:

The primary communication channel we will use is Julia Slack and Dr. Jakub Mitura (MD, PhD) will be the individual responsible for all contact and mentoring throughout the project for regular updates and meetings.
Outside of Slack, email will be used to handle communications with GSoD organizers and administrators with Jakub Mitura's email being: jakub.mitura14@gmail.com.
Volunteers will also be available for communication on the Slack on an as-needed basis.
Additionally, project updates will be given through the Julia Health Slack Channel which is where the majority of JuliaHealth communication takes place between members, users, and the rest of the Julia community.

Project Budget

Note

You can include your budget in your proposal or as a separate link. If your budget is fewer than ten items, we recommend including it in your proposal.

Budget item Amount Running total
Technical writer $4000 $4000
Volunteer (x4) $500 $2000
Swag (3 shirts and 10 sticker packs) $125
TOTAL   $6125

Additional justifications:

• Volunteers: Please see the above section on Project Scope for details about selected volunteers
• Swag: is to create a more welcoming environment for our writer and volunteers
  • Sticker packs will also be given to welcome new contributors

Additional information:

Beyond the above proposal information, some additional notes about the composition of this project team:

Jacob Zelko was selected as a volunteer as he has a proven track record as a successful Google Summer of Code mentor for the past 3 years and is currently the Julia Organization's co-administrator for this years Google Summer of Code where he handles questions from both students and mentors.
Given his experience, Jacob will provide guidance to Jakub and Sneha as needed to make sure this project is well-aligned with general Google Open Source program goals.
Additionally, Jacob has a overseen many grants in the past through Google Summer of Code and former positions at Georgia Tech Research Institute and the Centers for Disease Control and will provide a valuable asset in answering any questions about the project scope.

Anshul Singhvi is a former Google Summer of Code student and has a vast swath of experience of working across the Julia ecosystem.
In particular, Anshul has membership with numerous Julia organizations and will be a crucial asset to not only what are best practices for documentation deployment but can also help with how to best unify JuliaHealth packages within JuliaHealth itself and potentially across the greater Julia landscape.
His insight will be crucial to mitigate any redundant work or answer oustanding questions to make sure this project is ran as effectively as possible.
Also, given Anshul's tremendous experience in delivering contract work, he will be key in making sure the metrics we investigate and report on for the case study in our final report will be done rigorously and to the best of the technical writer's ability given the data we have access to.

I added a strengthening section about additional information -- could you add a small piece about yourself there @jakubMitura14 ? this is to align with: https://developers.google.com/season-of-docs/docs/org-proposal-template

Finally, I increased the budget slightly for swag :-) I thought it would be a fun idea and is actually encouraged by Google here.

[jakubMitura14]

My bio

Researcher specialising in creating artificial intelligence models for medical imaging. Holds a doctorate in medical sciences with a thesis titled ‘The Role of Positron Emission Tomography Using Fluorodeoxyglucose in the Diagnosis of Vascular Prosthesis Infections.’ Additionally, holds a master’s degree in informatics with a specialisation in Big Data. Has authored scientific publications in the fields of medicine and artificial intelligence.

[cncastillo]

Hi ! Sorry, hopefully I am not too late for this. We have a few documentation task that would require some help.

https://github.com/JuliaHealth/KomaMRI.jl/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3Adocumentation

• Add Contributing Guidelines JuliaHealth/KomaMRI.jl#209
• Include steps for contributing using VSCode JuliaHealth/KomaMRI.jl#233
• Use PlutoStaticHTML.jl to export Pluto notebooks in documentation
  • Create Pluto example for fat_sat_low_field JuliaHealth/KomaMRI.jl#291
• Use Vitepress Documenter JuliaHealth/KomaMRI.jl#333
• Add multithreading usage in documentation JuliaHealth/KomaMRI.jl#307
• Missing citations in Figures of educational example JuliaHealth/KomaMRI.jl#272
• Review API Docstrings JuliaHealth/KomaMRI.jl#260
• Modify Literate Examples Generation JuliaHealth/KomaMRI.jl#251
• Documentation minor tasks JuliaHealth/KomaMRI.jl#69
• Automate figure generation with Literate JuliaHealth/KomaMRI.jl#226 (only works for examples)
• Include an adiabatic pulse example using Literate JuliaHealth/KomaMRI.jl#227